LASER: Large genome ASsembly EvaluatoR Academic Article uri icon

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abstract

  • BACKGROUND: Genome assembly is a fundamental problem with multiple applications. Current technological limitations do not allow assembling of entire genomes and many programs have been designed to produce longer and more reliable contigs. Assessing the quality of these assemblies and comparing those produced by different tools is essential in choosing the best ones. The QUAST program has become the current state-of-the-art in quality assessment of genome assemblies. The only drawback of QUAST is high time and memory usage for large genomes, e.g., over 4 days and 120 GB of RAM for a single human genome assembly. RESULTS: We introduce LASER, a new tool for assembly evaluation that improves greatly the speed and memory requirements of QUAST. For a human genome assembly, LASER is 5.6 times faster than QUAST while using only half the memory; one human genome assembly is evaluated in 17 hours instead of 4 days. The code of LASER is based on that of QUAST and therefore inherits all its features. CONCLUSIONS: Genome assembly evaluation is an essential step in assessing the quality of an assembly that is too often done improperly, in part due to significant resource consumption. With the introduction of LASER, proper evaluation can be performed efficiently.

publication date

  • December 2015